In my opinion, you could make a CEDH deck with almost any commander. The question would then be, "How effective is it?" I think in the case of Kruphix, we have to look at what he does and whether it advances a gameplan. His ability to give you an unlimited hand size is not an effect that is typically used or sought after in CEDH. If I draw 20-30 cards in a turn, I am looking to win that turn, even as a control deck. His second ability, which essentially stores mana between turns, also isn't particularly useful. The idea would be to generate vast amounts of mana, draw many cards, and win that turn. On top of all of this, he's a 5-mana casting cost. Other 5-mana commanders in the format are immediate win conditions and require an immediate response from your opponents. One example of this is Gitrog Monster.
If you wanted to make a control commander with these colors, certainly Thrasios + partner would be better in all regards.